Epy, he's talking about graphs like those used in graph theory. What you are talking about are called graphs of a function. Unlike graphs on a function, which are for modeling trends and linear relations, graphs in graph theory are for showing relations between nodes or vertices. Discrete math is the closest relative of CS in math, you should consider studying it. I know you've heard of Dijkstra's shortest path finding algo, it's a solution to the problem of path finding in graph theory. You've probably also heard of four color theorem, it is from graph theory.

The best thing I can think of, on the assumption that Matlab lets you do it (which I don't know), is to do a vector of vectors. (I get the sneaking suspicion that, for Matlab, a "vector of vectors" is really a matrix.)